He was apparently dead in the early script but not in the later drafts.
Here are some tweets from Devin Faraci about this.
devincf: Gordon isn't dead in the new DCEU. He was dead in a script about a year and a half ago, but they clearly rethought that.
devincf: Him being dead was only noted by the presence of a Jim Gordon memorial plaque. Unkilling him required no reshoots, no major changes.
devincf: I think it's a smart move for the future of solo Batfilms.
devincf: Anyway, they made a bunch of changes since that script, many that return things to the Goyer draft. The "knightmare" was in Goyer but
devincf: not the script I know. Dead Robin was in Goyer but not the script I know. The main beats remain from the script I know.
devincf: Anyway, I'm glad they changed it, that Gordon is alive and that JK Simmons is playing him.